static MolecularSequence.Builder |
MolecularSequence.builder() |
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MolecularSequence.Builder |
MolecularSequence.Builder.contained(java.util.Collection<Resource> contained) |
These resources do not have an independent existence apart from the resource that contains them - they cannot be
identified independently, and nor can they have their own independent transaction scope.
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MolecularSequence.Builder |
MolecularSequence.Builder.contained(Resource... contained) |
These resources do not have an independent existence apart from the resource that contains them - they cannot be
identified independently, and nor can they have their own independent transaction scope.
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MolecularSequence.Builder |
MolecularSequence.Builder.coordinateSystem(java.lang.Integer coordinateSystem) |
Convenience method for setting coordinateSystem .
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MolecularSequence.Builder |
MolecularSequence.Builder.coordinateSystem(Integer coordinateSystem) |
Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or
starting at 1 (1-based numbering, inclusive start and inclusive end).
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MolecularSequence.Builder |
MolecularSequence.Builder.device(Reference device) |
The method for sequencing, for example, chip information.
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MolecularSequence.Builder |
MolecularSequence.Builder.extension(java.util.Collection<Extension> extension) |
May be used to represent additional information that is not part of the basic definition of the resource.
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MolecularSequence.Builder |
MolecularSequence.Builder.extension(Extension... extension) |
May be used to represent additional information that is not part of the basic definition of the resource.
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protected MolecularSequence.Builder |
MolecularSequence.Builder.from(MolecularSequence molecularSequence) |
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MolecularSequence.Builder |
MolecularSequence.Builder.id(java.lang.String id) |
The logical id of the resource, as used in the URL for the resource.
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MolecularSequence.Builder |
MolecularSequence.Builder.identifier(java.util.Collection<Identifier> identifier) |
A unique identifier for this particular sequence instance.
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MolecularSequence.Builder |
MolecularSequence.Builder.identifier(Identifier... identifier) |
A unique identifier for this particular sequence instance.
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MolecularSequence.Builder |
MolecularSequence.Builder.implicitRules(Uri implicitRules) |
A reference to a set of rules that were followed when the resource was constructed, and which must be understood when
processing the content.
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MolecularSequence.Builder |
MolecularSequence.Builder.language(Code language) |
The base language in which the resource is written.
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MolecularSequence.Builder |
MolecularSequence.Builder.meta(Meta meta) |
The metadata about the resource.
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MolecularSequence.Builder |
MolecularSequence.Builder.modifierExtension(java.util.Collection<Extension> modifierExtension) |
May be used to represent additional information that is not part of the basic definition of the resource and that
modifies the understanding of the element that contains it and/or the understanding of the containing element's
descendants.
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MolecularSequence.Builder |
MolecularSequence.Builder.modifierExtension(Extension... modifierExtension) |
May be used to represent additional information that is not part of the basic definition of the resource and that
modifies the understanding of the element that contains it and/or the understanding of the containing element's
descendants.
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MolecularSequence.Builder |
MolecularSequence.Builder.observedSeq(java.lang.String observedSeq) |
Convenience method for setting observedSeq .
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MolecularSequence.Builder |
MolecularSequence.Builder.observedSeq(String observedSeq) |
Sequence that was observed.
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MolecularSequence.Builder |
MolecularSequence.Builder.patient(Reference patient) |
The patient whose sequencing results are described by this resource.
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MolecularSequence.Builder |
MolecularSequence.Builder.performer(Reference performer) |
The organization or lab that should be responsible for this result.
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MolecularSequence.Builder |
MolecularSequence.Builder.pointer(java.util.Collection<Reference> pointer) |
Pointer to next atomic sequence which at most contains one variant.
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MolecularSequence.Builder |
MolecularSequence.Builder.pointer(Reference... pointer) |
Pointer to next atomic sequence which at most contains one variant.
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MolecularSequence.Builder |
MolecularSequence.Builder.quality(java.util.Collection<MolecularSequence.Quality> quality) |
An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred
quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).
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MolecularSequence.Builder |
MolecularSequence.Builder.quality(MolecularSequence.Quality... quality) |
An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred
quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).
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MolecularSequence.Builder |
MolecularSequence.Builder.quantity(Quantity quantity) |
The number of copies of the sequence of interest.
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MolecularSequence.Builder |
MolecularSequence.Builder.readCoverage(java.lang.Integer readCoverage) |
Convenience method for setting readCoverage .
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MolecularSequence.Builder |
MolecularSequence.Builder.readCoverage(Integer readCoverage) |
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed
sequence.
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MolecularSequence.Builder |
MolecularSequence.Builder.referenceSeq(MolecularSequence.ReferenceSeq referenceSeq) |
A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
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MolecularSequence.Builder |
MolecularSequence.Builder.repository(java.util.Collection<MolecularSequence.Repository> repository) |
Configurations of the external repository.
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MolecularSequence.Builder |
MolecularSequence.Builder.repository(MolecularSequence.Repository... repository) |
Configurations of the external repository.
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MolecularSequence.Builder |
MolecularSequence.Builder.specimen(Reference specimen) |
Specimen used for sequencing.
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MolecularSequence.Builder |
MolecularSequence.Builder.structureVariant(java.util.Collection<MolecularSequence.StructureVariant> structureVariant) |
Information about chromosome structure variation.
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MolecularSequence.Builder |
MolecularSequence.Builder.structureVariant(MolecularSequence.StructureVariant... structureVariant) |
Information about chromosome structure variation.
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MolecularSequence.Builder |
MolecularSequence.Builder.text(Narrative text) |
A human-readable narrative that contains a summary of the resource and can be used to represent the content of the
resource to a human.
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MolecularSequence.Builder |
MolecularSequence.toBuilder() |
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MolecularSequence.Builder |
MolecularSequence.Builder.type(SequenceType type) |
Amino Acid Sequence/ DNA Sequence / RNA Sequence.
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MolecularSequence.Builder |
MolecularSequence.Builder.variant(java.util.Collection<MolecularSequence.Variant> variant) |
The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.
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MolecularSequence.Builder |
MolecularSequence.Builder.variant(MolecularSequence.Variant... variant) |
The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.
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